 ../
|
AAinfo.java
|
524
(12 years ago)
by duarte:
Fixed reading od PDB files. We hope now to be catching all possible errors present in original PDB files, plus we read correctly CASP TS files:
- now reading (and requiring) TARGET record for CASP TS files
- now we always have (and require) a sequence (possibly with ? or X) for all cases: PdbfilePdb, CaspRRFileRIGraph, FileRIGraph.
- in PDB files we throw format exceptions for: insertion codes, residue numbers <=0, non-ascending order of residue numbers in atom lines, when residues of SEQRES seq and ATOM seq don't match. In addition we warn when starting residue in ATOM lines is >100
- we allow PDB files without a HEADER, i.e. only ATOM lines
New fields in Pdb for CAPS identifiers: passed all the way down to RIGraphs in getGraph()
|
|
AIGEdge.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
AIGNode.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
AIGraph.java
|
659
(12 years ago)
by stehr:
Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
|
|
Alignment.java
|
641
(12 years ago)
by stehr:
added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
|
|
AlignmentConstructionError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
Box.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
CaspRRFileData.java
|
644
(12 years ago)
by duarte:
New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
|
|
CaspRRFileRIGraph.java
|
543
(12 years ago)
by duarte:
Now forcing i<j in CASP RR files (as specified by the CASP RR format)
|
|
CatalSiteSet.java
|
514
(12 years ago)
by filippis:
Latest scop and csa versions updated.
|
|
CatalyticSite.java
|
503
(12 years ago)
by filippis:
createGraphDb:
-scop_graph table added
-!!!!residue serial fields (num, i_num, j_num) are changed to unsigned
!!!!ProtStructGraph:
-interSSE variable added
-getResidueSerial abstract method added
-restrictContactsBetweenSs method added
!!!!AIGraph:
-getResidueSerial method added
RIGraph:
-!!!!getResidueSerial method added
-scop graphs are written to db correctly
-interSSE variable taken into account for CR db field
DbRIgraph:
-changes made so to be able to read from db using a scop id
-interSSE and minSeqSep are set now in get_db_graph_info()
-!!!!FIXED BUG:fullLength in read_graph_from_db is not set to the size of the serials2nodes TreeMap instead of the maximum serial in serials2nodes. It was giving wrong result for scop graphs.
testDbRIGraph added:
It reads one graph from a source db based either
-on pdbcode, chaincode and graph properties or
-on scop id and graph properties or
-on a graph id
and it writes the graph to a destination db.
Pdb:
-unused scop regions are now removed in restrictToScopDomain
-unused residues are also removed from resser2pdbresser, pdbresser2resser, resser2allrsa, resser2scrsa, resser2consurfhsspscore, resser2consurfhsspcolor, catalSiteSet
-!!!!sequence is reset to scop sequence and fullLength to the length of the scop sequence
CatalSiteSet:
- removeCatalSiteRes(int resser) method added
CatalyticSite:
-remRes(int resser) method added
Scop:
-remove(ScopRegion e) method added
genDbGraph:Comments only added to demonstrate new functionality.
-comment added to show how to use restrictContactsBetweenSs
-comment added to show how to use restrictToScopDomain
-runDssp now is always run and not only when mode != "GRAPH". This has been changed since now the contact range might depend on the ss assignment (restrictContactsBetweenSs) and we want to ensure consistent results
-runNaccess moved to the bottom so it is always run last. In this way if restrictToScopDomain is used, we don't have to run naccess twice.
|
|
CiffileFormatError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
CiffilePdb.java
|
639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
|
|
ConformationsNotSameSizeError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
ContactType.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
DbRIGraph.java
|
639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
|
|
EC.java
|
502
(12 years ago)
by stehr:
EC, CatalSiteSet: added typing to some iterators to avoid eclipse warning
Interval: added typing to Comparator to avoid eclipse warning
|
|
ECRegion.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
FastaFileFormatError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
FileFormatError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
FileRIGraph.java
|
551
(12 years ago)
by duarte:
Fixed bug: now reading/writing #MODEL field in contact map files
In Pdb writeAtomLines now prints a nicer header with source info depending on source: file or db
|
|
FileTypeGuesser.java
|
550
(12 years ago)
by stehr:
changed header of contact map file from #AGLAPPE... to #CMVIEW...; when reading, both are accepted to ensure backwards compatibility
|
|
GraphFileFormatError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
GraphIODb.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
GraphIOGDLFile.java
|
635
(12 years ago)
by duarte:
Changed default gravity value and default IDENTITY_SCORE for similarity graph
|
|
GraphIdNotFoundError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
IntPairComparator.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
IntPairSet.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
Interval.java
|
515
(12 years ago)
by stehr:
Interval: allow spaces in residue selection strings
RIGNbhood: added method getNeighbors
|
|
IntervalSet.java
|
592
(12 years ago)
by stehr:
fixed one null pointer bug and some spelling mistakes
|
|
MaxClusterRunner.java
|
585
(12 years ago)
by stehr:
added method calculateSequenceIndependentMatrix()
|
|
MsdsdInconsistentResidueNumbersError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
MsdsdPdb.java
|
639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
|
|
NbhProbDistribution.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
NbhoodBackgrnd.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PairwiseAlignmentConverter.java
|
517
(12 years ago)
by duarte:
Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this.
NOTE: graph averaging hasn't been tested after the change
|
|
PairwiseSequenceAlignment.java
|
575
(12 years ago)
by filippis:
reconstruct:
-rmsd to mirrored pdb has been added in the report file
Pdb:
-comment for outputing missing atoms added
PairwiseSequenceAlignment:
-constructor with parameters openScore and extendScore for the gaps has been added
|
|
Pdb.java
|
672
(12 years ago)
by filippis:
chechScop now looks also for chain A in scop.cla when pdbChainCode is NULL
|
|
PdbChainCodeNotFoundError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PdbCodeNotFoundError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PdbLoadError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PdbaseInconsistencyError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PdbasePdb.java
|
639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
|
|
PdbfileFormatError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PdbfilePdb.java
|
661
(12 years ago)
by stehr:
Now enforcing that atom serials have to be in ascending order
|
|
PirFileFormatError.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
PredEval.java
|
563
(12 years ago)
by duarte:
Added new convenience method printSummary
|
|
ProtStructGraph.java
|
659
(12 years ago)
by stehr:
Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
|
|
RIGCommonNbhood.java
|
512
(12 years ago)
by duarte:
Added getCommanSeparatedResSerials to RIGCommonNbhood
|
|
RIGEdge.java
|
546
(12 years ago)
by duarte:
New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble
|
|
RIGEnsemble.java
|
614
(12 years ago)
by stehr:
PdbfilePdb: catching previously unhandled NumberFormatException, added method setSequence() to override sequence read from file (needed for Casp prediction where 'real' sequence is known but residues may be missing in prediction)
RIGEnsemble: many changes
|
|
RIGNbhood.java
|
529
(12 years ago)
by spriya:
Drop sequence comparison in compare. Now we compare only length
New method getSize in RIGNbhood to be used instead of size that returns neighborhood size + 1
|
|
RIGNode.java
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
RIGraph.java
|
644
(12 years ago)
by duarte:
New feature: averageGraph now also writes out the CASP RR file (if -c specified) for the average graph at Cb 8.
Made a bit prettier the CASP RR output: now contacts sorted and weights with only 2 decimal figures.
|
|
Scop.java
|
589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
|
|
ScopRegion.java
|
589
(12 years ago)
by duarte:
New classes Template, TemplateList to be used in homology modelling pipeline.
Modified BlastUtils to use TemplateList class
|
|
SecStrucElement.java
|
639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
|
|
SecondaryStructure.java
|
639
(12 years ago)
by duarte:
Implemented parsing of PsiPred secondary structure prediction files in SecondaryStructure class.
New member in SecondaryStructure: sequence. Constructor must pass the sequence now, changed all references.
New method in Alignment to print a "graphical" matching of secondary structures.
|
|
Template.java
|
651
(12 years ago)
by duarte:
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
|
|
TemplateList.java
|
651
(12 years ago)
by duarte:
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
|
|
aapairsBounds.dat
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
|
contactTypes.dat
|
492
(12 years ago)
by duarte:
Copied the aglappe-jung branch into trunk.
|
